I use Handbrake to convert files from any source to ipad compatible.. then works fine in standard ipad player.
Can also try ipad presets here but these do result in very large files (~1.5GB).

Not sure if it converts mkv though - havent tried yet. But seems to do most I've asked of it.

Edit: a quick check on the site says it does do mkv

This post has been edited by mbcx4jrh: Aug 19 2010, 11:36 AM